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Bioinformatics Databases and Applications Available for Glycobiology and Glycomics

  • René Ranzinger
  • Kai Maaß
  • Thomas LüttekeEmail author
Chapter

Abstract

Bioinformatics for glycobiology is still considered to be in its infancy. Nevertheless, there are various applications and databases available for glycoscientists by now. This article summarizes the problems that glycoinformatics is facing and gives an overview of the existing resources, including web portals, databases and tools. Software for structure input and display, for processing of analytical data, for prediction and analysis of glycosylation sites, and applications related to carbohydrate 3D structures are described. Special emphasis is put on GlycomeDB, a project that aims to integrate all freely available carbohydrate structure data already stored in databases, and the taxonomic annotation of these structures, into one resource. By this means it allows researchers to locate data in many databases without having to learn the different query types and carbohydrate notations used in the individual resources.

Keywords

Bioinformatics Carbohydrate database GlycomeDB Glycan Glycosylation sites Automatic annotation 3D structure Analytical software Carbohydrate software tools 

Abbreviations

CQS

complex query system

ETL-Process

Extract-Transform-Load-Process

GU

glucose unit

GT

glycosyltransferase

HPLC

high performance liquid chromatography

MS

mass spectrometry

MD

molecular dynamics

NMR

nuclear magnetic resonance

REST

representational state transfer

PDB

protein data bank

SOAP

simple object access protocol

2-AB

2-aminobenzamide

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© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.Complex Carbohydrate Research CentreThe University of GeorgiaAthensUSA
  2. 2.Department of chemistry, Institute of Inorganic and Analytical ChemistryJustus-Liebig University GießenGlessenGermany
  3. 3.Faculty of Veterinary Medicine, Institute of Biochemistry and EndocrinologyJustus-Liebig University GießenGießenGermany

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